Clearly, a zygote does not harbor any microbes. As it develops, and the alimentary canal tissue is differentiated, I logically assume that there is still no microbial activity in the fetus's gut. I'm thus also assuming that the commencement of microbial activity in the intestines occurs after birth, but when, and how?

Do newborn babies just happen to ingest only certain e.g., E.coli strains? Is the gut a selective environment in which only certain E.coli strains develop?

Are there any mechanisms to ensure that harmful bacteria do not initially reside in the gut? Is a newborn's digestive tract particularly unstable and ineffective until the proper microbes are established?

2 Answers
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The gastrointestinal tract of a normal fetus is sterile. During birth and rapidly thereafter, bacteria from the mother and the surrounding environment colonize the infant's gut. Immediately after vaginal delivery, babies may have bacterial strains derived from the mothers' feces in the upper gastrointestinal tract.[15] Infants born by caesarean section may also be exposed to their mothers' microflora, but the initial exposure is most likely to be from the surrounding environment such as the air, other infants, and the nursing staff, which serve as vectors for transfer.[16] The primary gut flora in infants born by caesarean delivery may be disturbed for up to six months after birth, whereas vaginally born infants take up to one month for their intestinal microflora to be well established.[citation needed] After birth, environmental, oral and cutaneous bacteria are readily transferred from the mother to the infant through suckling, kissing, and caressing. All infants are initially colonized by large numbers of E. coli and streptococci. Within a few days, bacterial numbers reach 108 to 1010 per gram of feces.[16][17] During the first week of life, these bacteria create a reducing environment favorable for the subsequent bacterial succession of strict anaerobic species mainly belonging to the genera Bifidobacterium, Bacteroides, Clostridium, and Ruminococcus.[18] Breast-fed babies become dominated by bifidobacteria, possibly due to the contents of bifidobacterial growth factors in breast milk.[19][20] In contrast, the microbiota of formula-fed infants is more diverse, with high numbers of Enterobacteriaceae, enterococci, bifidobacteria, Bacteroides, and clostridia.[21][22] By the second year of life, the fecal microflora resemble that of adults (wiki source).

The initiation of gut flora come from maternal cervical and vaginal flora (Bezirtzoglou, 1997)1. These predominantly include facultative anaerobes (e.g., Staphylococcus, Enterobacteriaceae and Streptococcus). Birth by caesarean section can cause problems because these bacteria are not passed on in the usual manner.

Vael et al. (2011)2 found an association between early gut flora and obesity later in life

High intestinal Bacteroides fragilis and low Staphylococcus
concentrations in infants between the age of 3 weeks and 1 year were
associated with a higher risk of obesity later in life.

suggesting that monitoring or alterations of gut flora might be effective in reducing rates of obesity.